2-102454108-T-C

Variant names:

• chr2-102454108-T-C
• rs917997

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.777 in 152,156 control chromosomes in the GnomAD database, including 46,922 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.78 (46922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118067 AN: 152036 Hom.: 46879 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.755

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.777 AC: 118159 AN: 152156 Hom.: 46922 Cov.: 32 AF XY: 0.771 AC XY: 57333 AN XY: 74382

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.757

Alfa AF: 0.754 Hom.: 94110

Bravo AF: 0.766

Asia WGS AF: 0.580 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs917997; hg19: chr2-103070568; COSMIC: COSV51825029;